My TARDIS Your Doctor
by KateAmeliaJUdd
Summary: Is it really so bad that all the Doctor wants is to have her back? What will it cost to have her around again? Why can't he give her up? With Amy and Rory once again stuck in the Doctor's decisions. Is it to late to save her? To save them?
1. Chapter 1

**Okay so I wanted to get a story written after I had a million different theories about Doctor Who. I have a feeling that Hello was not what the TARDIS wanted to say. So yeah I am following through with some theories. I am sure that in a few days there will be so many fan fictions about this within the next few days. So yeah, besides theories are cool. Just like bow ties, fezzes, Stetsons and bunk beds. So sit back with some Jammie Dodgers and a cup of tea and hopefully review and let me know what you think. Set straight after 'The Doctor's Wife' **

The Doctor simply just leapt around the TARDIS and flicked a few switches here and there. It seemed like the TARDIs and he had a much better relationship now than before. Something that he was rather pleased about. She certainly worked more with him instead of just sending him where he needed to go rather than just where he wanted to go. Sometimes it was better to go where one wanted than where one was needed. He let out a small sigh as he rested against the console itself and closed his eyes for a few moments. Just letting his thoughts run wild.

Was it all a bad thing that he just wanted the TARDIS back? The human her. Somewhere along the line he had developed a really close bond with her and if anything he just wanted to have that back again. he felt like he understood the TARDIS more now. he just needed to by her side again and maybe hold her hand. It wasn't the same talking to a machine anymore. Now that he experienced her as human he couldn't just act normally around her. It wasn't long before a series of beeps started coming from the console somewhere. The Doctor instantly spun around and pressed his hand to the console, gently stroking her. "It's okay. Everything is going to be fine. I am here, your Doctor is here. I am not going anywhere." he said in a soothing voice.

It was only really then that he had a strange and wild thought. what did he care if it brought about the end of something. if it ripped a whole in the Universe or destroyed the TARDIS as he knew it. He had lived his whole life taking chances so why should now be any different. If the TARDIS wanted to see the world then he was going to make that happen for her. Only not just by having the old blue Police Box stand in one place until he returned. He had to bring the human her back. maybe it was just House getting into his head and manipulating him into thinking that he wanted her around him again. he couldn't just never see her again. Maybe it would be easier to leave things as they were, he wasn't sure if he could deal with the fact that he might just once again lose her. Yet that was a chance that he was willing to take.

"No need to worry or get yourself all flustered. Trust me I'm your Doctor and I am coming back for you" he whispered to the Console once again stroking it rather affectionatly with his hand. Maybe he wasn't in his right mind. Yet that was probably something that was the best thing at the moment. If he was then he would only talk himself out of it.

Amy Pond walked into the console room. As usual she was wearing one of her insanely short skirts. Her ginger hair was loose upon her shoulders. She ran a hand through it and looked towards her best friend. She could instantly tell that he was up to something, or at least that there was something on his mind. She pressed her lips together and bounded down the stairs to his side. One of her hands rested against his shoulder, making him jump slightly.

"Ah, you gave me a fright then. Morning Pond. Where is Rory, normally he is like your little puppy dog, never leaving your side"

His words just made her smile, he never did fail to just make her smile. "Morning. He is still asleep. Anyway enough about him what is bothering you? Don't say nothing. I know you and I know that there is something bothering you"

"Okay I won't say that there is nothing. Although if I tell you what I am up to you will only talk me out of it. So I am keeping my mouth shut. Now go and get up your husband and I will see you outside."

Before Amy could say anything else the Doctor had ran towards the TARDIS doors and stepped outside. She just sighed slightly. Sometimes she really did worry about him. Something was screaming at her to just leave Rory where he was and follwo him outside without her husband. She could always just leave a note for him and let him know where they had gotten off to. After staying put for a few moments she came to the conclusion that she didn't have enough time to spare to use up getting Rory up. She knew exactly what he could be like in the mornings sometimes. There had to be some scrap paper and a pen around somewhere. She noticed on of Rory's jackets hanging over the banister and reached into the pockets. Finally she managed to locate a pen. NOw she had the task of finding some paper. She sighed slightly. Now she was starting to think that maybe she would have been better off getting Rory up. Although that couldn't be help now she dropped the pen to glass floor of the TARDIS and ran towards the doors. Something was really up with the Doctor and she fully intended to find out what it was. Rory would surely locate them soon enough. Even if he did take to searching the TARDIS for them. She reached her hand into the pocket of her jacket and felt something rather small in there. it felt like the bulb of a Christmas tree light. She stared at it for a moment. Where had this come from? It took a moment for her to remember. It was that little chip the Doctor had placed into their hands whilst battling against the Silence. She placed it upon the console and ran out after the Doctor. The only thing that she could hope for was that it would work and Rory would hear her voice. if not then she was just going to have to deal with things later.

What was he thinking? He most certainly wasn't thinking straight. All he wanted right now was to be with her again. He made his way through the grime and muck and towards the place that she had been captured in. If only he had thought this through before he had made rational decisions. He only hoped that the TARDIS would know what to do. She was so much more cleverer when it came to things like this. If she was stuck then so was he and this had all been one big mistake and a hell of a wasted trip. "TARDIS? TARDIS old girl, you down here?" he found himself whispering. Really there wasn't much need to speak. They did share a telepathic bond. A bond that could be broken. There was just no reply. he stopped dead in his tracks for a few moments as he heard footsteps behind him. He swallowed and took a step back into the shadows. No one should be around here. There was no one left to be around. There had been no sign of any life. Yet the TARDIS had given a strong sense of itself. So he couldn't be far. The footsteps seemed to just die down and the Doctor could only put it down to the fact that it was probably just House messing around. After all if he was here before it was all defeated by his own TARDIS then it was probably hanging around somewhere.

After continuing down the corridor for what seemed like another half an hour he had to give up and turn back. Obviously there wasn't anyone or anything down there. Maybe the TARDIS had picked up a wrong signal? that had to be the answer. Yet the moment he turned his back and took a few steps up the corridor again in an attempt to get out of this place heard a voice. A voice calling his name. How could he ignore it? Something was telling him that he recognised it.

"Hello. Is there someone there. I warn you I am armed." he called out. of course the only weapon that he had was his Sonic Screwdriver and even that couldn't be thought of a weapon. Yet the owner of the voice didn't need to know that. Those footsteps behind him started up again. The Doctor turned around and practically ran down the corridor, only if he was heading towards the voice and away from the footsteps or towards the footsteps and way from the voice he had no idea. He refused to admit that he was lost.

Amy was starting to feel a little alone and a little lost at the moment. She knew that she should have woken up Rory. Now she just wished that he was here with her. She just had no idea what direction the Doctor had headed in or whether she was heading into the same direction. Everything was dark. She could see just a little way in front of her and yet that about all.

The red head screamed as she walked into something or someone. Yet she instantly relaxed as she realised it was only the Doctor.

"Amy! What are you doing here? I thought I told you to wake up Rory" his hands were rested upon her shoulder and it was that alone that made Amy suddenly feel protected again. She knew that even if he had no idea what he was doing then she was going to be fine as long as they were together.

"I was worried about you. I had to follow you. Rory will be fine. He is in the TARDIS even he isn't stupid enough to get himself hurt in there." she replied with a smile. "Now what are you up to? I don't like this place it reminds me of being alone in the dark"

"Well I might as well tell you. it isn't really like you can get out of it now. I think we are trapped. I am getting back the TARDIS. My TARDIS. My human TARDIS. You hear that old girl. I am coming to get you."

Rory opened his eyes and let out a small sigh. At least the Doctor hadn't given them bunk beds this time. he might have thought that bunk beds were cool and yet he himself certainly didn't and he was rather sure that Amy didn't either. He turned over to face her side of the bed and was rather surprised to see that she wasn't there. he sat up and glanced around the room. At first just thinking that maybe she was hanging around the room somewhere and getting herself changed. Only when he could see her he just rolled his eyes. Knowing his luck she was off in the TARDIS Console room with the Doctor. He knew that she often just said that he was her best friend and nothing more than that, but Rory did think that the Doctor was so much better suited to her than he was. They had the same fire in their personality and they just got on so well. Yet that was probably just him worrying to much. She wouldn't have married him if she didn't love him, right?

He yawned slightly and rubbed his eyes before climbing out of bed and pulling on some clothes, before heading out into the corridor and making the left turn to the Console room. Although it was all to quiet in there. It was only as he came straight into the huge room that he realised the colum in the centre wasn't moving, so that had to mean that they were not actually in flight. So where were the pair of them? Would they really have left the TARDIS without him? maybe the Doctor would have done just that only he was sure that Amy wouldn't. Unless she had an exceptionally good reason. No, they had to be around the TARDIS somewhere.

Not wanting to waste another second of his time hanging around the TARDIS to wait for them to come back he turned to head back through the corridors again to search for the two of them.

_"RORY!"_

Now that made him turn around and run into the Console room again. He had just heard her voice from inside there he knew that much. He was sure that he hadn't just been imagining it. He ran a hand through his hair and tried to determine where they could be. Or at least where Amy was.

_"RORY!"_

He heard her voice again. She sounded terrified. Only what was he supposed to do. it was clar to him that she wasn't in the console room. So how the hell had he heard her voice coming from it. It was only after a few moments of panicking that he noticed a red flashing light upon the console. He raced towards and it and picked up. Although almost dropping it as he heard her voce coming from it once again. Only this time she seemed to be talking to someone.

_"Where is he? What have you done to him? You can't fool me. I know who you are. I remember you. I REMEMBER. You can't erase yourselves from my memory again"_

"Amy! Can you hear me? Where are you? I'm coming. If you can hear me stay where you are I am coming. I will find you" Rory found himself saying. Although he had a strong feeling that she couldn't hear a word of what he was saying. Something was telling him that, just like the last time she had left behind this little red flashing chip, it was simply just one way.

**Okay so I know that chapter didn't really make sense and that there wasn't much Rory in there for all you Rory loving fans although I do promise that things will star to make sense. Plus there is going to be a lot more Rory in the story as it progresses. I do love Rory and yet I am not really sure I can get his character any good. let me know how I am doing. Also I do apologise for any mistakes. I wrote this chapter rather quickly. Anyone fancy being a beta? Review and let me know what you think and you can have some Jammie Dodger and you choice of a Bow tie, A fezz or a Stetson.**

**Future chapters should also be longer.**


	2. Chapter 2

**Wow! I didn't think I would get so many Alerts to this story. Although I just wan to take the time to thank all of you for it. I really do appreciate it. I am also sorry for the lateness of this chapter. Things have just been rather busy recently. Although there should be a few chapters written up in the next day or so to make up for it. Once again thank you to all of for your support it is what keeps me writing.**

Rory really just had no idea what he could do. Was there anything that he could do? He just didn't know. Only running around like a headless chicken trying to find either Amy or the Doctor was probably not really the best of things to be doing at the moment. He just had to try and get his head around things and not go running into anything. He wasn't really all that used to all this time travel and stuff just yet. maybe he was getting his head in a spin over nothing.

Yes that just had to be it. He was getting his head into a spin over nothing, right? No, there was no way that Amy would get herself all up tight and well almost scared like she had just been. He knew that she could always hear him and that he was never ever going to give up on her. No matter where she was he was always going to find her.

Yet where exactly he was going he had no idea in the slightest. he was just walking around and just hoping that he was headed in the right direction. Even if he didn't find her straight away and he found the doctor instead would that be something? Would the doctor even be able to help? Rory just had no idea. As plain normal without Amy by his side to help out with things he was just totally lost and had literally not a clue where he was supposed to be going or what he was supposed to be doing. He had certainly never realised just how much he did rely on that girl until now. Sure she was his wife, but had he really relied upon her to do something as simple as not getting to panicky in a situation where things just seemed to be getting out of hand, rather much like they were now.

Rory practically jumped out his skin as he felt a hand upon his arm. he spun around and came face to with the girl who the Doctor had claimed to be the TARDIS. was this all just some dream? Or was he really once again face to face to face with her. Suddenly that just didn't matter. Either way she was the TARDIS and if anyone could help him, better than the absent Doctor could, find Amy.

"Hello. I know that word now. Hello it is nice to finally see you again. Oh so many years I have been on this planet. Just trapped here, waiting for the Doctor, my Doctor. Your name? It was... Rufus...or was it Roland?"

Rory just smiled slightly and rolled his eyes slightly. "It's Rory. Although I have a favour to ask you. can you help me? I need to find Amy. the ginger one that was here with me last time. She and the Doctor are somewhere and they left me in the TARDIS. Well the big blue Box TARDIS."

"Yes, well they are in the place where the darkness is the only comfort and the place where nightmares come to haunt and keep the smile upon your face"

The confusion must have shown in Rory's face. he had no idea what she was going on about. If anything the Doctor made more sense that she did. yet he wasn't really about to argue with her. As far as he could make out she knew where Amy and the Doctor were and that was good enough for him.

The Doctor's eyes opened and he instantly sat up. "Amy!" he called out and yet got no reply. What was going on here? Where the hell was he for a start? he jumped to his feet and reached into his jacket pocket to remove the Sonic Screwdriver. It seemed like he was going to have to try and work out a few things. Although his main worry was that Amy was alright. it then came to his mind that Rory could be in trouble if he stepped outside and into this place. Hopefully he hadn't left the TARDIS yet. Placing it onto the right setting he used the Sonic Screwdriver to lock the TARDIS doors, there was now way that anything was getting in or out that place until he unlocked it again. He sighed slightly and started to look for a way out or at least a way to turn on the lights. It was so dark and if anything it was just annoying. he hated not being able to see what he was dealing with. It was so much easier to be able to see the enemy he was talking to. Not that there was anyone in here right now. At least not that he knew of. Everything was totally silent. The only sound was the buzzing of the screwdriver and the sound of his rather extensive breathing. Was it strange that he was starting to feel rather claustrophobic in this place right now. It just didn't seem like the room was all that big. There just had to be something going on in here. He just had to work out what it was. There had never yet been an alien or human for that matter that he hadn't been able to defeat or help. Not something that he was going to make a change to now. A small room was not going to defeat him.

A few minutes seemed to pass before the doctor was aware of a slight breathing sound. A breathing sound that wasn't his own. he held his breath, just to make sure and sure enough the breathing continued. "Hello? Anyone there? Look I am not going to hurt you. I'm the Doctor. I can help you"

He listened for a reply and yet nothing came. His eyes looked around him just trying to locate any kind of moving. Anything that might give him a sign that something else was sharing the room with him.

Something was there with her. Amy knew that much. She was far to scared to move or say anything that might give away her location to the occupant of the room. How had she gotten in here. The last thing that she was aware of was shouting screaming at something that had taken her away from the Doctor. it was all happening again. just simply walking through a door and she was trapped. Trapped in her own fears. There was a set of yellow eyes staring straight towards her through the darkness. Who did they belong to? Could whoever it was even see her? She had no idea. Her heart was racing in her chest. This place was beyond creepy and was really starting to scare her. It was strange how the only things that she could think about was that there was something following her. Something looming over her. She felt like all her nightmares were becoming reality and all of them were trapped up in this room. Was that even possible? Sure ever since travelling with the Doctor she had started to come to terms with the fact that almost everything and anything could happen. But the things in her nightmares coming to life around her was something else. She felt something brushing up against her arm and forced herself not to gasp. She needn't worry about jumping or even so much as flinching since her her body seemed to be way to scared to move. Something had to be done. She had to get out and she had to get out fast. Otherwise she had a feeling that something in this room was going to get to vivid.

A few moments later and the lighting started to flicker, not that there was any light in place as it was. yet there was defiantly some flicking of light. Amy managed to shuffle along the wall that her back was pressed up against and into a shadowy corner. Yet whether or not that was a good idea or not she wasn't really sure.

**Sorry this chapter is shot. I have just run out of ideas and it would have been longer had ai not chosen to have the Doctor in the room of darkness. i just wasn't sure what else to write. I am hoping that the next chapter will answer some questions, plus that it is will be longer. Once again I am sorry that it is so short and sorry for taking so long to get this chapter up. Sorry for any stupid little mistakes I wrote this rather quickly. Please review and let me know what you think.**


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